This method was developed at the FDA’s Center for Food Safety and Applied Nutrition for GenomeTrakr Laboratories; however, this protocol was written to be broadly applicable for any wastewater sequence data submission to NCBI.
This protocol covers the last step of making your data public at NCBI. Specifically, it provides the steps to establish a new NCBI submission environment for your laboratory, including the creation of new BioProject(s) and submission groups. Once these are step up, the protocol steps through the process for submitting raw reads to SRA and sample metadata to BioSample through the Submission portal.
For new submitters, there's quite a bit of groundwork that needs to be established before a laboratory can start its first data submission. We recommend that one person in the laboratory take a few days to get everything set up in advance of when you expect to do your first data submission.
If you need a pipeline for frequent or large volume submissions, follow Step 1 in this protocol to get your NCBI submission environment established, then contact gb-admin@ncbi.nlm.nih.gov to set up an account for submitting through the API. V2: minor edits to the BioSample and SRA templates
V3: Adapted the protocol to be more broadly applicable to submitters outside of FDA's wastewater project. Updates were also made to both metadata templates, including a new attribute to the SRA metadata template, called "enrichment_kit".
V4: updates to BioSample and SRA templates: expanded picklists, addition of specimen processing attributes for including replicate info, and the removal of target_extract attribute for reporting level of target found in the sample.
V5: includes guidance for submitting BioSamples with no linked sequence data.
V6: Updated templates. BioSample: added picklist for PCR concentration units. SRA: added new quality control attributes.
V7: SRA and BioSample template updates
V8: SRA template updates. "Illumina COVIDSeq Assay" added to library_preparation_kit, "QIAseq DIRECT SARS-CoV-2 - Boosted" added to amplicon_PCR_primer_scheme, "low coverage of characteristic mutations" added to quality_control_issues. minor edits to the protocol are also included in this update.
V10: Minor edits to generalize the protocol for broader usage. Picklist updates made to the BioSample and SRA templates.